A Revised Set of Potentials for Beta-turn Formation in Proteins

Overview

Journal Protein Sci

Specialty Biochemistry

Date 1994 Dec 1

PMID 7756980

Citations 252

Authors

E G Hutchinson

J M Thornton

Affiliations

Soon will be listed here.

Abstract

Three thousand eight hundred ninety-nine beta-turns have been identified and classified using a nonhomologous data set of 205 protein chains. These were used to derive beta-turn positional potentials for turn types I' and II' for the first time and to provide updated potentials for formation of the more common types I, II, and VIII. Many of the sequence preferences for each of the 4 positions in turns can be rationalized in terms of the formation of stabilizing hydrogen bonds, preferences for amino acids to adopt a particular conformation in phi, psi space, and the involvement of turn types I' and II' in beta-hairpins. Only 1,632 (42%) of the turns occur in isolation; the remainder have at least 1 residue in common with another turn and have hence been classified as multiple turns. Several types of multiple turn have been identified and analyzed.

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References

Venkatachalam C . Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers. 1968; 6(10):1425-36. DOI: 10.1002/bip.1968.360061006. View

McDonald I, Thornton J . Satisfying hydrogen bonding potential in proteins. J Mol Biol. 1994; 238(5):777-93. DOI: 10.1006/jmbi.1994.1334. View

Lewis P, Momany F, Scheraga H . Chain reversals in proteins. Biochim Biophys Acta. 1973; 303(2):211-29. DOI: 10.1016/0005-2795(73)90350-4. View

Chou P, Fasman G . Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry. 1974; 13(2):211-22. DOI: 10.1021/bi00699a001. View

Bernstein F, Koetzle T, Williams G, Meyer Jr E, Brice M, Rodgers J . The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977; 112(3):535-42. DOI: 10.1016/s0022-2836(77)80200-3. View

Chou P, Fasman G . Beta-turns in proteins. J Mol Biol. 1977; 115(2):135-75. DOI: 10.1016/0022-2836(77)90094-8. View

Steigemann W, Weber E . Structure of erythrocruorin in different ligand states refined at 1.4 A resolution. J Mol Biol. 1979; 127(3):309-38. DOI: 10.1016/0022-2836(79)90332-2. View

Isogai Y, NEMETHY G, Rackovsky S, Leach S, Scheraga H . Characterization of multiple bends in proteins. Biopolymers. 1980; 19(6):1183-210. DOI: 10.1002/bip.1980.360190607. View

Richardson J . The anatomy and taxonomy of protein structure. Adv Protein Chem. 1981; 34:167-339. DOI: 10.1016/s0065-3233(08)60520-3. View

10.

Artymiuk P, Blake C . Refinement of human lysozyme at 1.5 A resolution analysis of non-bonded and hydrogen-bond interactions. J Mol Biol. 1981; 152(4):737-62. DOI: 10.1016/0022-2836(81)90125-x. View

11.

Tainer J, Getzoff E, Beem K, Richardson J, Richardson D . Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase. J Mol Biol. 1982; 160(2):181-217. DOI: 10.1016/0022-2836(82)90174-7. View

12.

Furey Jr W, Wang B, Yoo C, Sax M . Structure of a novel Bence-Jones protein (Rhe) fragment at 1.6 A resolution. J Mol Biol. 1983; 167(3):661-92. DOI: 10.1016/s0022-2836(83)80104-1. View

13.

Rees D, Lewis M, Lipscomb W . Refined crystal structure of carboxypeptidase A at 1.54 A resolution. J Mol Biol. 1983; 168(2):367-87. DOI: 10.1016/s0022-2836(83)80024-2. View

14.

Bode W, Papamokos E, Musil D . The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Structural analysis, subtilisin structure and interface geometry. Eur J Biochem. 1987; 166(3):673-92. DOI: 10.1111/j.1432-1033.1987.tb13566.x. View

15.

Rose G, Gierasch L, Smith J . Turns in peptides and proteins. Adv Protein Chem. 1985; 37:1-109. DOI: 10.1016/s0065-3233(08)60063-7. View

16.

Kabsch W, Sander C . Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983; 22(12):2577-637. DOI: 10.1002/bip.360221211. View

17.

Acharya R, Fry E, Stuart D, Fox G, Rowlands D, Brown F . The three-dimensional structure of foot-and-mouth disease virus at 2.9 A resolution. Nature. 1989; 337(6209):709-16. DOI: 10.1038/337709a0. View

18.

Wilmot C, Thornton J . Beta-turns and their distortions: a proposed new nomenclature. Protein Eng. 1990; 3(6):479-93. DOI: 10.1093/protein/3.6.479. View

19.

Veerapandian B, Cooper J, Sali A, Blundell T . X-ray analyses of aspartic proteinases. III Three-dimensional structure of endothiapepsin complexed with a transition-state isostere inhibitor of renin at 1.6 A resolution. J Mol Biol. 1990; 216(4):1017-29. DOI: 10.1016/S0022-2836(99)80017-5. View

20.

Orengo C, Brown N, Taylor W . Fast structure alignment for protein databank searching. Proteins. 1992; 14(2):139-67. DOI: 10.1002/prot.340140203. View